2 Answers
2

Some phones' partitions have a separate partition for the kernel (often called "boot") that is separate from the one that holds /system.

Unzip the CynanogenMod update.zip - there should be a boot.img inside. If you have fastboot and know how to use it, you can flash boot.img with ./fastboot flash boot /path/to/boot.img(You will need to be S-OFF for this; sounds like you are.)

Another option is to go back to stock & flash CM again. If you're flashing CM over top of itself you may be able to get away without wiping /data (you may still want to wipe /cache)